SMTL ID : 2yye.1

Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

10 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: D.53, D.92, D.228 Ligands: CO.2, APC.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, A:D.92, A:D.228, H2O.3, H2O.5 CO.2: 6 residues within 4Å: Chain A: D.69, D.92 Ligands: CO.1, CO.3, APC.6, CO.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.69, A:D.92, H2O.3, H2O.6 CO.3: 7 residues within 4Å: Chain A: D.53, T.67, V.68, D.69, D.92 Ligands: CO.2, APC.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, A:T.67, A:D.92, H2O.1, H2O.3 CO.4: 7 residues within 4Å: Chain A: D.52, D.53, A.95, M.96, I.164, T.165, C.226 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.52, A:D.53, A:A.95, A:I.164, A:C.226 CO.5: 5 residues within 4Å: Chain A: H.141 Chain B: V.68, D.69 Ligands: CO.9, APC.13 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.141, B:D.69, H2O.9 CO.7: 5 residues within 4Å: Chain A: V.68, D.69 Chain B: H.141 Ligands: CO.2, APC.6 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.141, A:D.69, H2O.5 CO.8: 5 residues within 4Å: Chain B: D.53, D.92, D.228 Ligands: CO.9, APC.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.53, B:D.92, B:D.228, H2O.6, H2O.11 CO.9: 6 residues within 4Å: Chain B: D.69, D.92 Ligands: CO.5, CO.8, CO.10, APC.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:D.92, H2O.10, H2O.11 CO.10: 7 residues within 4Å: Chain B: D.53, T.67, V.68, D.69, D.92 Ligands: CO.9, APC.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.53, B:T.67, B:D.92, H2O.6, H2O.6 CO.11: 7 residues within 4Å: Chain B: D.52, D.53, A.95, M.96, I.164, T.165, C.226 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.52, B:D.53, B:A.95, B:I.164, B:C.226

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.6: 23 residues within 4Å: Chain A: K.25, L.31, Q.32, L.35, I.50, G.51, D.52, D.53, D.69, D.92, T.230, G.231, F.232 Chain B: A.105, S.107, G.139, G.140, H.141, T.142 Ligands: CO.1, CO.2, CO.3, CO.7 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:K.25, A:K.25, A:G.51, A:T.230, A:G.231, B:S.107, B:G.140, B:T.142, B:T.142 Water bridges: A:D.52, A:D.52, A:D.53, A:D.69, B:L.138, B:G.140, B:T.142 Salt bridges: A:K.25, B:H.141 APC.13: 21 residues within 4Å: Chain A: A.105, S.107, G.139, G.140, H.141, T.142 Chain B: L.31, L.35, I.50, G.51, D.52, D.53, D.69, D.92, T.230, G.231, F.232 Ligands: CO.5, CO.8, CO.9, CO.10 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:S.107, A:G.140, A:T.142, B:G.51, B:G.51, B:T.230, B:G.231 Water bridges: A:L.138, A:G.140, A:T.142, B:L.31, B:D.52, B:D.52, B:D.69, B:F.232 Salt bridges: A:H.141

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 5 residues within 4Å: Chain B: K.188, E.192, K.269, I.270, Y.271 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.192, B:K.269, B:K.269, B:Y.271 Water bridges: B:K.188, B:K.188 Salt bridges: B:K.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itoh, Y. et al., Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs. J.Mol.Biol. (2009)

Release Date

2008-04-29

Peptides

Selenide, water dikinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Selenide, water dikinase

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